Open larsoner opened 4 years ago
sounds good !
From a meeting with @jasmainak it seems like a tentative workable plan is:
.surf
files to subjects_dir/subject/...
somewhere (surf/subcort.lh.*
?)mne.setup_subcortical_source_space
, e.g., if the spacing
parameter no longer makes sense.SourceMorph
Good next steps would be:
sample
mne.setup_source_space
from it, then forward, then inverse. Then visualize traces with matplotlib
for now
It turns out (I think!) you can take just about any subcortical ROI and turn it into a surface using a few FreeSurfer commands:
The
.smooth
surfaces look reasonable for the MNEsample
subject:And they can be inflated to a sphere (so that they can be subdivided via ico/oct) with:
Here is a starting API proposal:
setup_source_space(..., surf='...')
allowsurf
to be a list/tuple of names in aseg.mgz, not justsurf/
files. The default would stay'white'
, which is an alias for (as would bepial
and other cortical surfaces)('lh.white', 'rh.white')
to create a cortical surface source space.FIFF.FIFFV_MNE_SURF_LEFT_HEMI = 101
for left, 102 for right; maybe we should use1000+aseg_value
for any non-cortical surface, and left/right hemi would keep their "special" / exceptional values of 101 and 102 (their numbers inaseg.mgz
appear to be 2 or 3 and 41 or 42).kind
for aSourceSpaces
with just these surfaces would be not'surf'
(keep this for cortical surf source spaces only) but instead'subcortical_surf'
or something. And combinations of cortical surf + subcortical surf would be, as usual,'mixed'
.fsaverage
and use FreeSurfer commands to align the surfaces (make.sphere
instead of just.qsphere
surfaces). Now thatmake_morph_maps
is not horribly slow anymore, creating the morph maps on the fly might be acceptable since these surfaces in general will have way fewer vertices.